snATACseq analysis with ArchR.
ArchR pre-filters the cells using 2 metrics:
Counts
| Sample | Cells_Pass_Filter | Cells_dropped | Total_Frags | Median_Frags | Median_TSS_Enrichment |
|---|---|---|---|---|---|
| 510_FC | 7011 | 219 | 141701588 | 15242 | 14.259 |
| 611_FC | 3869 | 161 | 89911016 | 16830 | 11.868 |
| 993_FC | 5273 | 207 | 62967252 | 5871 | 9.037 |
Doublet removal
Post-doublet removal numbers are the final cell numbers moving forward.
| Sample | Pre_DoubRem | Post_DoubRem | pc_cells_removed |
|---|---|---|---|
| 510_FC_ATAC | 7011 | 6520 | 7.003281 |
| 611_FC_ATAC | 3869 | 3720 | 3.851124 |
| 993_FC_ATAC | 5273 | 4995 | 5.272141 |
Pre-filter plots
TSS enrichment vs. log10(Number of fragments) - these are the pre-filtered results
If you want to compare these results to others studies check out page 4 of the ArchR supplementary document.
Post-filter plots
TSS enrichment vs. log10(Number of fragments) plot - all samples combined
Fragment size plot
TSS plot
Ridge plot
Cluster mappings
| RNA | ExN-4 | RG-1 | ExN-2 | N-undef | InN-1 | RG-1 | ExN-3 | InN-3 | RG-1 | ExN-2 | MG | InN-2 | ExN-5 | RG-2 | InN-2 | ExN-2 |
| ATAC | C1 | C15 | C8 | C10 | C4 | C11 | C12 | C9 | C16 | C7 | C13 | C5 | C2 | C14 | C6 | C3 |
Cell counts
UMAP